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Structure-activity studies of MDM2/MDM4-binding stapled peptides comprising non-natural amino acids
Analyse Structure-activity studies of MDM2/MDM4-binding stapled peptides comprising… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XXK
- Type
- protein
- Length
- 209 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; Hydrocarbon stapled peptide…
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- 0EH, NH2
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 95 | 44% helix, 17% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 94 | 44% helix, 17% strand | Q00987 |
| C, D | Hydrocarbon stapled peptide thc-ser-phe-0EH-glu-tyr-6CW- ala-leu-leu-MK8-NH2 | protein | 10 | 50% helix, 0% strand | — |
Ligands and binding sites
- 0EH · (2R)-2-amino-2-methylnonanoic acid · ligand · 2 copies · chains A, B, C, D
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.79 | 0.93 | 26 | 0EH |
Interfaces
6 interfaces between chains.
- B–D · 623 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 617 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 592 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 274 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 273 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 modified (covalent ligand, nonstandard).
Compared structures
- 5XXK · Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q00987
- Elsewhere: RCSB PDB 5XXK · PDBe 5XXK · UniProt Q00987
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